[Bioperl-l] Bio::Location::Fuzzy CoordinatePolicy questions

Chris Fields cjfields at uiuc.edu
Thu Sep 7 16:28:38 EDT 2006


> I guess there's arguments either way, depending on what you interpret
> the contract to to_FTstring() to be.
> 
> If you argue that to_FTstring() needs to return a GenBank feature
> table-compliant string then you cannot leave it to the
> CoordinatePolicy to decide on the end points that satisfy compliance.
> 
> Conversely, if you argue that to_FTstring() may return a string which
> is GenBank feature table-compliant only in terms of formatting, then
> there is freedom of interpretation as to what the end points could be.
> 
> I'm leaning to the former, as there isn't a universal standard for
> feature location formatting. Or if there is, then this method doesn't
> implement it. It really is there to return a GenBank-compliant
> string. Or so I think - other opinions welcome, and are likely to exist.
> 
> 	-hilmar

The default coordinate policy for Bio::Location::Atomic is
WidestCoordPolicy, which is GenBank-compliant (i.e. it passes tests when set
explicitly).  That should work by default as Location::Fuzzy is-a
Location::Atomic.  It would then be left up to the user to change it if they
want something non-compliant (NarrowestCoordPolicy or AvWithinCoordPolicy or
whatever). 

Anyway, I managed to fix the bug w/o having to manipulate the coordinate
policy.  It passes all tests so I'll go ahead and commit it.  

Chris



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